The court filing in the case of Mr. Cohen, President Trump’s self-described fixer, indicates for the first time that others at Mr. Trump’s company had a role in the financial arrangements used to silence women who claimed that they had affairs with him, after the hush money payments were made.

Two senior Trump Organization executives had involvement in the financial arrangements, according to the 22-page court filing.

Separately, one or more members of the 2016 Trump campaign were cited as having worked to identify stories about Mr. Trump’s romantic entanglements “so they could be purchased and their publication avoided,” the filing said.

Mr. Cohen, the filing said, “coordinated with one or more members of the campaign, including through meetings and phone calls,” about the nature and timing of the payments, which were made to influence the election.

The people are not identified in the documents.

It is unclear whether they face any sort of legal risk, but the filing does raise questions about the conduct of the Trump Organization itself.

Mr. Cohen paid Stephanie Clifford, an adult film actress, $130,000 to ensure that she would not speak publicly about an affair she said she had with Mr. Trump, and he was then reimbursed through the Trump Organization.

The court filing, which outlines campaign finance violations and other crimes to which Mr. Cohen pleaded guilty, traces the reimbursement through the company.

It begins when Mr. Cohen requested it, submitting a bank statement from a shell company he created to mask the payment’s connection to Mr. Trump, and ends with the Trump Organization’s monthly disbursements to Mr. Cohen.

The reimbursement was processed using unusual accounting practices, a nonexistent retainer agreement, and equally unusual tax decisions, helped along the way by Trump Organization executives who, it seemed, at best, looked the other way.

A representative of the Trump Organization declined to comment on Wednesday.

Mr. Cohen said in federal court in Manhattan on Tuesday that Mr. Trump had told him to arrange payments to two women during the 2016 campaign to keep them from going public about affairs they said they had with Mr. Trump. Mr. Cohen pleaded guilty to breaking campaign finance law, as well as tax fraud and making false statements to a bank related to his personal business interests.

Cohen’s Plea Deal and Charges

The plea agreement between Michael D. Cohen and prosecutors along with the charges to which Mr. Cohen pleaded guilty.

30 pages, 4.84 MB

Mr. Cohen made the statement about Mr. Trump’s role in the payments to the two women — Ms. Clifford and a former Playboy playmate — as he pleaded guilty to two campaign finance crimes.

One of those charges stemmed from the $130,000 payment he made to Ms. Clifford, who is better known as Stormy Daniels, before the 2016 presidential election.

Prosecutors said Trump Organization executives were involved in reimbursing Mr. Cohen for that payment, accepting his phony invoices that listed it as a legal expense. The other charge concerned a complicated arrangement in which a tabloid bought the rights to the story about the former Playboy model, Karen McDougal, then killed it.

Michael D. Cohen, President Trump’s former lawyer, has pleaded guilty to violating federal campaign finance laws and has implicated Mr. Trump. Here is how their relationship has evolved.CreditCreditAndres Kudacki for The New York Times

“I think the allegations reveal that executives in the Trump Organization — more than one, and not clear how many more than one — were involved in funneling the payments to Stormy Daniels and may have significant legal exposure as a result of that,” she said, even though their actions came after the fact.

“Obviously, they are trying to hide something,” she added. “There’s a normal way to do this and then there’s the way they did it.”

The company recorded the reimbursement to Ms. Clifford as legal fees, which legal experts characterized as unusual.

Mr. Cohen paid Ms. Clifford $130,000, but he was ultimately reimbursed $420,000 by the Trump Organization.

Here’s why: Mr. Cohen received a $60,000 bonus, and the company allocated about $180,000 to cover the taxes that Mr. Cohen had to pay on the hush money.

There was also an additional $50,000 that Mr. Cohen received after putting in a claim for “tech services.”

That related to work that Mr. Cohen “solicited” from a technology company during the campaign, the court filing said.

Several current and former prosecutors and criminal defense lawyers said that if the officials at the Trump Organization were aware of what the payments were for, they could possibly be criminally culpable.

And they said that if the $420,000 in payments to Mr. Cohen, which were recorded as legal expenses, were written off as a tax deduction, as would be the general practice, it could lead to criminal tax charges.

But one person with knowledge of the company’s operations and familiar with the details surrounding the payments said neither of the two executives were aware of what the payments were for and that the payments were not deducted from the Trump Organization’s taxes.

The person said only the first two of the 12 monthly $35,000 payments to Mr. Cohen were paid by a trust that owns the company; the other 10 were paid from Mr. Trump’s personal accounts.

But the person, who would only discuss the payments on the condition of anonymity, could not say who approved the reimbursement; why it was approved if no one knew what it was for; why the payments were recorded as legal expenses; and why, even though they were recorded as such, they were not deducted from the company’s taxes.

Ms. Ware, the criminal tax lawyer, said, “It would be highly unusual to record it as legal fees and then not deduct it.”

The court papers and the officials who announced the case did not address whether Mr. Cohen’s guilty plea brought the investigation to a close or whether it remains ongoing.

Indeed, a staple of law enforcement news conferences — a senior official intoning, “the investigation is continuing” — was noticeably absent on Tuesday when the deputy United States attorney, Robert Kuhzami, concluded his remarks announcing Mr. Cohen’s guilty plea.